From 1993ec9150d839786649414389793aa5114f2ed1 Mon Sep 17 00:00:00 2001
From: Kay-Robert Dormann <kay-robert.dormann@pkm.tu-darmstadt.de>
Date: Fri, 1 Nov 2024 12:36:10 +0100
Subject: [PATCH 1/2] WIP: single clusters added to cluster.identify

---
 amep/cluster.py | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/amep/cluster.py b/amep/cluster.py
index e4dced0..a60be2d 100644
--- a/amep/cluster.py
+++ b/amep/cluster.py
@@ -1036,18 +1036,18 @@ def identify(
     particle_idx  = set(np.arange(len(coords)))
     clustered_idx = set()
 
-    n = 0
+    cluster_id = 0
     for cl in sorted_clusters:
-
         for i in cl:
-            idx[i] = n
+            idx[i] = cluster_id
             clustered_idx.add(i)
-
-        n += 1
+        cluster_id += 1
 
     # add leftover single particles
     for k in particle_idx - clustered_idx:
-        idx[k] = n
-        n += 1
+        idx[k] = cluster_id
+        sorted_clusters.append([k])
+        cluster_id += 1
+    idx=np.array(idx, dtype=int)
 
     return sorted_clusters, idx

From 92442e6f6903fbc3f05e269a3666063e235cb2bf Mon Sep 17 00:00:00 2001
From: Kay-Robert Dormann <kay-robert.dormann@pkm.tu-darmstadt.de>
Date: Fri, 1 Nov 2024 13:49:50 +0100
Subject: [PATCH 2/2] fixes #85

---
 amep/cluster.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/amep/cluster.py b/amep/cluster.py
index a60be2d..2052b10 100644
--- a/amep/cluster.py
+++ b/amep/cluster.py
@@ -940,7 +940,8 @@ def identify(
     sorted_clusters : list
         List of lists, where each list contains the indices of the particles
         that belong to the same cluster. The list is sorted by the number of
-        particles in each cluster.
+        particles in each cluster. Single particles are also included as
+        clusters in this list.
     idx : numpy.ndarray
         Array of shape (N,) containing the cluster ID for each particle. N is 
         the total number of particles.